build

bump #225

	name: build

	on: [push]

	jobs:
	build:

	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ["3.10"]

	steps:
	- uses: actions/checkout@v3
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v3
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install CD-Hit
	run: \|
	wget https://github.com/weizhongli/cdhit/releases/download/V4.8.1/cd-hit-v4.8.1-2019-0228.tar.gz
	tar -xzvf cd-hit-v4.8.1-2019-0228.tar.gz
	cd cd-hit-v4.8.1-2019-0228
	make
	chmod u+x cd-hit
	pwd
	- name: Export cd-hit path
	run: \|
	echo /home/runner/work/rnaglib/rnaglib/cd-hit-v4.8.1-2019-0228 >> $GITHUB_PATH
	- name: Install US-align
	run: \|
	wget https://zhanggroup.org/US-align/bin/module/USalign.cpp
	g++ -static -O3 -ffast-math -o USalign USalign.cpp
	chmod u+x ./USalign
	- name: Export USalign path
	run: \|
	echo /home/runner/work/rnaglib/rnaglib/ >> $GITHUB_PATH
	- name: Install rna-align
	run: \|
	wget https://zhanggroup.org/RNA-align/bin/RNAalign.tar.bz2
	tar -xvjf RNAalign.tar.bz2
	cd RNAalign
	g++ -O3 -ffast-math -o RNAalign RNAalign.cpp -static
	chmod u+x ./RNAalign
	pwd
	- name: Export RNAalign path
	run: \|
	echo /home/runner/work/rnaglib/rnaglib/RNAalign >> $GITHUB_PATH
	- name: Test with pytest
	run: \|
	echo $PATH
	which RNAalign
	which cd-hit
	pip install -r requirements_test.txt
	pip install coverage
	coverage run --source src/rnaglib -m pytest
	coverage report -m
	coverage xml
	- name: Upload Coverage
	uses: codecov/codecov-action@v2
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	files: coverage.xml
	flags: pytest
	name: rnaglib
	fail_ci_if_error: true
	verbose: true

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